Theis Lab

single-cell-best-practices

https://www.sc-best-practices.org

scvelo

RNA Velocity generalized through dynamical modeling

cellrank

CellRank: dynamics from multi-view single-cell data

scib

Benchmarking analysis of data integration tools

sfaira

data and model repository for single-cell data

single-cell-transformer-papers

chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

destiny

R package for single cell and other data analysis using diffusion maps

scTab

spapros

Python package for Probe set selection for targeted spatial transcriptomics.

geome

neural_organoid_atlas

Reproducibility repository for the Human Neural Organoid Atlas publication

2019_Strunz

Reproducibility repo accompanying Strunz et al. "Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis". Nat Commun. 2020.

cellrank_notebooks

Tutorials and examples for CellRank.

scatac_poisson_reproducibility

ehrapy-tutorials

Tutorials for ehrapy

flowVI

flowVI: Flow Cytometry Variational Inference

cellrank2_reproducibility

CellRank 2's reproducibility repository.

perturbation-metrics

atlas-feature-selection-benchmark

Code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use

HRCA-reproducibility

Scripts related to the Human Retina Cell Atlas (Chen / Theis labs).

spatial_atlas_ssl

Self-supervised learning for mask inpainting on large spatial atlasses such as the BICCN 2.0 data.

pertpy-datasets

Dataset preparation for pertpy

sparsecca

Python implementations for Sparse CCA

transcription_factor_activity

ehrapy-reproducibility

ELS_analysis

Repository for code and notebooks for the analysis of the Early life adversity shapes social subordination and cell-type-specific transcriptomic (Kos et al., 2023) paper.

integraph

scarches-1

Reference mapping for single-cell genomics